Linkage and mapping analyses of the no glue egg gene Ng in the silkworm (Bombyx mori L.) using simple sequence repeats (SSR) markers

In the silkworm, Bombyx mori, no glue egg is mainly controlled by Ng (No glue) gene, which is located on the 12th chromosome. Owning to a lack of crossing over in females, reciprocal backcrossed F1 (BC1) progenies were used for linkage analysis and mapping of the Ng gene based on the simple sequence repeats (SSR) linkage map using silkworm strains H9 and P50, which are Ng mutant and normal to egg, respectively. The Ng gene was found to be linked to three SSR markers. Using a reciprocal BC1M cross, we constructed a linkage map of 36.4 cM, with Ng mapped at 15.9 cM and the nearest SSR marker at a distance of 7.4 cM. Based on fine genome map of domesticated silkworm (B. mori), the result of Kaikoblast show that the physical distance between the near markers (containing Ng gene) is 181.7 Kb. Further analysis show that BGIBMGA005833, BGIBMGA005835 and BGIBMGA005836 are closer to Ng, and the BGIBMGA005835 is nearest to Ng, which physical distance is 44 Kb.Key words: Gene location, linkage analysis, microsatellite, Ng, silkworm

Phenoloxidase activity acts as a mosquito innate immune response against infection with semliki forest virus

Several components of the mosquito immune system including the RNA interference (RNAi), JAK/STAT, Toll and IMD pathways have previously been implicated in controlling arbovirus infections. In contrast, the role of the phenoloxidase (PO) cascade in mosquito antiviral immunity is unknown. Here we show that conditioned medium from the Aedes albopictus-derived U4.4 cell line contains a functional PO cascade, which is activated by the bacterium Escherichia coli and the arbovirus Semliki Forest virus (SFV) (Togaviridae; Alphavirus). Production of recombinant SFV expressing the PO cascade inhibitor Egf1.0 blocked PO activity in U4.4 cell- conditioned medium, which resulted in enhanced spread of SFV. Infection of adult female Aedes aegypti by feeding mosquitoes a bloodmeal containing Egf1.0-expressing SFV increased virus replication and mosquito mortality. Collectively, these results suggest the PO cascade of mosquitoes plays an important role in immune defence against arboviruses

Getting “Just Deserts” or Seeing the “Silver Lining”: The Relation between Judgments of Immanent and Ultimate Justice

People can perceive misfortunes as caused by previous bad deeds (immanent justice reasoning) or resulting in ultimate compensation (ultimate justice reasoning). Across two studies, we investigated the relation between these types of justice reasoning and identified the processes (perceptions of deservingness) that underlie them for both others (Study 1) and the self (Study 2). Study 1 demonstrated that observers engaged in more ultimate (vs. immanent) justice reasoning for a "good" victim and greater immanent (vs. ultimate) justice reasoning for a "bad" victim. In Study 2, participants' construals of their bad breaks varied as a function of their self-worth, with greater ultimate (immanent) justice reasoning for participants with higher (lower) self-esteem. Across both studies, perceived deservingness of bad breaks or perceived deservingness of ultimate compensation mediated immanent and ultimate justice reasoning respectively. © 2014 Harvey and Callan

The Escherichia coli transcriptome mostly consists of independently regulated modules

Underlying cellular responses is a transcriptional regulatory network (TRN) that modulates gene expression. A useful description of the TRN would decompose the transcriptome into targeted effects of individual transcriptional regulators. Here, we apply unsupervised machine learning to a diverse compendium of over 250 high-quality Escherichia coli RNA-seq datasets to identify 92 statistically independent signals that modulate the expression of specific gene sets. We show that 61 of these transcriptomic signals represent the effects of currently characterized transcriptional regulators. Condition-specific activation of signals is validated by exposure of E. coli to new environmental conditions. The resulting decomposition of the transcriptome provides: a mechanistic, systems-level, network-based explanation of responses to environmental and genetic perturbations; a guide to gene and regulator function discovery; and a basis for characterizing transcriptomic differences in multiple strains. Taken together, our results show that signal summation describes the composition of a model prokaryotic transcriptome

Knowledge of general practitioners about nasopharyngeal cancer at the Puskesmas in Yogyakarta, Indonesia

<p>Abstract</p> <p>Background</p> <p>Nasopharyngeal carcinoma (NPC) is one of the leading causes of cancer death in Indonesia. At initial diagnosis, 80% of the patients present with advanced stage disease. In Indonesia, primary medical care is generally provided by the health care centres; named Puskesmas. The lack of knowledge of various aspects of NPC of the General practitioners (GPs) working in these centers might contribute to the diagnostic delay. The aim of this study was to assess the knowledge of these GPs on different aspects of NPC including symptoms, risk factors and incidence.</p> <p>Methods</p> <p>One hundred six GPs in the Puskesmas in the Yogyakarta province were subjected to a questionnaire on different aspects of NPC based on literature and interviews with Head and Neck Surgeons.</p> <p>Results</p> <p>All GPs approached participated and in total 106 questionnaires were filled in. All participants were aware of NPC as a disease and 89% confirmed that it is a serious problem in Indonesia. However, 50% of the participants believed NPC has a low incidence in their region. The question on early symptoms gave a mean 4.2 answers of which 50% were incorrect.</p> <p>The GPs provided a total of 318 answers when asked for the risk factors of NPC, 75% of which were incorrect. Fifty seven GPs (54%) stated that they did not receive sufficient education on NPC at the university and insufficient knowledge was gained during daily practice. Ninety-two percent of the GPs were interested in additional education, preferably in form of lectures, meetings or folders.</p> <p>Conclusion</p> <p>This study revealed that GPs in the Puskesmas in Yogyakarta lack knowledge on all aspects of NPC. This is an important finding as NPC is endemic in Indonesia and the Puskesmas are the institutions which provide primary medical health care in the country. Further education of the GPs in these endemic areas could be a first step to increase the rate of early detection. Therefore, we suggest 1) to conduct a medical awareness campaign for GPs on the most important subjects concerning NPC, and 2) as soon as NPC awareness among GPs has risen, provide further education on the risk factors, the early symptoms and the incidence, education to the community. We propose to extend this study to other areas in Indonesia (i.e. Jakarta, Surabaya, Central Java), using models that have been developed in Yogyakarta.</p

Two novel human cytomegalovirus NK cell evasion functions target MICA for lysosomal degradation

NKG2D plays a major role in controlling immune responses through the regulation of natural killer (NK) cells, αβ and γδ T-cell function. This activating receptor recognizes eight distinct ligands (the MHC Class I polypeptide-related sequences (MIC) A andB, and UL16-binding proteins (ULBP)1–6) induced by cellular stress to promote recognition cells perturbed by malignant transformation or microbial infection. Studies into human cytomegalovirus (HCMV) have aided both the identification and characterization of NKG2D ligands (NKG2DLs). HCMV immediate early (IE) gene up regulates NKGDLs, and we now describe the differential activation of ULBP2 and MICA/B by IE1 and IE2 respectively. Despite activation by IE functions, HCMV effectively suppressed cell surface expression of NKGDLs through both the early and late phases of infection. The immune evasion functions UL16, UL142, and microRNA(miR)-UL112 are known to target NKG2DLs. While infection with a UL16 deletion mutant caused the expected increase in MICB and ULBP2 cell surface expression, deletion of UL142 did not have a similar impact on its target, MICA. We therefore performed a systematic screen of the viral genome to search of addition functions that targeted MICA. US18 and US20 were identified as novel NK cell evasion functions capable of acting independently to promote MICA degradation by lysosomal degradation. The most dramatic effect on MICA expression was achieved when US18 and US20 acted in concert. US18 and US20 are the first members of the US12 gene family to have been assigned a function. The US12 family has 10 members encoded sequentially through US12–US21; a genetic arrangement, which is suggestive of an ‘accordion’ expansion of an ancestral gene in response to a selective pressure. This expansion must have be an ancient event as the whole family is conserved across simian cytomegaloviruses from old world monkeys. The evolutionary benefit bestowed by the combinatorial effect of US18 and US20 on MICA may have contributed to sustaining the US12 gene family

Impact of chemotherapy for HIV-1 related lymphoma on residual viremia and cellular HIV-1 DNA in patients on suppressive antiretroviral therapy

The first cure of HIV-1 infection was achieved through complex, multimodal therapy including myeloablative chemotherapy, total body irradiation, anti-Thymocyte globulin, and allogeneic stem cell transplantation with a CCR5 delta32 homozygous donor. The contributions of each component of this therapy to HIV-1 eradication are unclear. To assess the impact of cytotoxic chemotherapy alone on HIV-1 persistence, we longitudinally evaluated low-level plasma viremia and HIV-1 DNA in PBMC from patients in the ACTG A5001/ALLRT cohort on suppressive antiretroviral therapy (ART) who underwent chemotherapy for HIV-1 related lymphoma without interrupting ART. Plasma HIV-1 RNA, total HIV-1 DNA and 2-LTR circles (2-LTRs) in PBMC were measured using sensitive qPCR assays. In the 9 patients who received moderately intensive chemotherapy for HIV-1 related lymphoma with uninterrupted ART, low-level plasma HIV-1 RNA did not change significantly with chemotherapy: median HIV-1 RNA was 1 copy/mL (interquartile range: 1.0 to 20) pre-chemotherapy versus 4 copies/mL (interquartile range: 1.0 to 7.0) post-chemotherapy. HIV-1 DNA levels also did not change significantly, with median prechemotherapy HIV-1 DNA of 355 copies/106 CD4+ cells versus 228 copies/106 CD4+ cells post-chemotherapy. 2-LTRs were detectable in 2 of 9 patients pre-chemotherapy and in 3 of 9 patients post-chemotherapy. In summary, moderately intensive chemotherapy for HIV-1 related lymphoma in the context of continuous ART did not have a prolonged impact on HIV-1 persistence. © 2014 Cillo et al

Elevational species richness gradients in a hyperdiverse insect taxon: a global meta-study on geometrid moths

AIMS: We aim to document elevational richness patterns of geometrid moths in a globally replicated, multi-gradient setting, and to test general hypotheses on environmental and spatial effects (i.e. productivity, temperature, precipitation, area, mid-domain effect and human habitat disturbance) on these richness patterns. LOCATION: Twenty-six elevational gradients world-wide (latitudes 28° S to 51° N). METHODS: We compiled field datasets on elevational gradients for geometrid moths, a lepidopteran family, and documented richness patterns across each gradient while accounting for local undersampling of richness. Environmental and spatial predictor variables as well as habitat disturbance were used to test various hypotheses. Our analyses comprised two pathways: univariate correlations within gradients, and multivariate modelling on pooled data after correcting for overall variation in richness among different gradients. RESULTS: The majority of gradients showed midpeak patterns of richness, irrespective of climate and geographical location. The exclusion of human-affected sampling plots did not change these patterns. Support for univariate main drivers of richness was generally low, although there was idiosyncratic support for particular predictors on single gradients. Multivariate models, in agreement with univariate results, provided the strongest support for an effect of area-integrated productivity, or alternatively for an elevational area effect. Temperature and the mid-domain effect received support as weaker, modulating covariates, while precipitation-related variables had no explanatory potential. MAIN CONCLUSIONS: Despite the predicted decreasing diversity–temperature relationship in ectotherms, geometrid moths are similar to ants and salamanders as well as small mammals and ferns in having predominantly their highest diversity at mid-elevations. As in those comparative analyses, single or clear sets of drivers are elusive, but both productivity and area appear to be influential. More comparative elevational studies for various insect taxa are necessary for a more comprehensive understanding of elevational diversity and productivity

Observation of a ppb mass threshoud enhancement in \psi^\prime\to\pi^+\pi^-J/\psi(J/\psi\to\gamma p\bar{p}) decay

The decay channel $\psi^\prime\to\pi^+\pi^-J/\psi(J/\psi\to\gamma p\bar{p})$ is studied using a sample of $1.06\times 10^8$ $\psi^\prime$ events collected by the BESIII experiment at BEPCII. A strong enhancement at threshold is observed in the $p\bar{p}$ invariant mass spectrum. The enhancement can be fit with an $S$-wave Breit-Wigner resonance function with a resulting peak mass of $M=1861^{+6}_{-13} {\rm (stat)}^{+7}_{-26} {\rm (syst)} {\rm MeV/}c^2$ and a narrow width that is $\Gamma<38 {\rm MeV/}c^2$ at the 90% confidence level. These results are consistent with published BESII results. These mass and width values do not match with those of any known meson resonance.Comment: 5 pages, 3 figures, submitted to Chinese Physics

Evaluation of multiple variate selection methods from a biological perspective: a nutrigenomics case study

Genomics-based technologies produce large amounts of data. To interpret the results and identify the most important variates related to phenotypes of interest, various multivariate regression and variate selection methods are used. Although inspected for statistical performance, the relevance of multivariate models in interpreting biological data sets often remains elusive. We compare various multivariate regression and variate selection methods applied to a nutrigenomics data set in terms of performance, utility and biological interpretability. The studied data set comprised hepatic transcriptome (10,072 predictor variates) and plasma protein concentrations [2 dependent variates: Leptin (LEP) and Tissue inhibitor of metalloproteinase 1 (TIMP-1)] collected during a high-fat diet study in ApoE3Leiden mice. The multivariate regression methods used were: partial least squares “PLS”; a genetic algorithm-based multiple linear regression, “GA-MLR”; two least-angle shrinkage methods, “LASSO” and “ELASTIC NET”; and a variant of PLS that uses covariance-based variate selection, “CovProc.” Two methods of ranking the genes for Gene Set Enrichment Analysis (GSEA) were also investigated: either by their correlation with the protein data or by the stability of the PLS regression coefficients. The regression methods performed similarly, with CovProc and GA performing the best and worst, respectively (R-squared values based on “double cross-validation” predictions of 0.762 and 0.451 for LEP; and 0.701 and 0.482 for TIMP-1). CovProc, LASSO and ELASTIC NET all produced parsimonious regression models and consistently identified small subsets of variates, with high commonality between the methods. Comparison of the gene ranking approaches found a high degree of agreement, with PLS-based ranking finding fewer significant gene sets. We recommend the use of CovProc for variate selection, in tandem with univariate methods, and the use of correlation-based ranking for GSEA-like pathway analysis methods